Establishing a standardized and universally applicable set of nuclear-encoded markers for genome-wide multi-locus species delimitation of metazoans

建立一套标准化且普遍适用的核编码标记，用于后生动物的全基因组多位点物种界定

• 批准号: 350964009
• 负责人: Dr. Dirk Ahrens
• 金额: --
• 依托单位: Leibniz-Institut zur Analyse des Biodiversitätswandels (LIB)
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/350964009?language=en
• 关键词: Establishing; standardized; universally; applicable; set

In our project funded during phase I of the DFG SPP "TaxonOmics", we established a set of markers for nuclear barcoding of Metazoa that rests on genes that almost exclusively occur in single-copy in the genomes of animals (universal single copy genes — USCOs). Using target DNA enrichment, we assess applicability and strengths of USCOs for delimiting species on the example of selected groups of arthropods. In the second phase of the SPP, we plan to assess the robustness of the USCO barcoding approach and to compare its performance with that of COI barcoding. We are particularly interested in the susceptibly of USCOs for overestimating the true species diversity, a problem that COI barcoding is known to suffer from. For this purpose, we will increase the infraspecific geographic sampling relative to that in our preceding project, focusing on groups which were already investigated by us during phase I of the SPP: butterflies, cellar spiders, centipedes, chafer beetles, and hoverflies. We additionally plan to study gene flow— something that would not be feasible with the classical barcoding approach. All bioinformatic steps required to conduct the above research will be integrated in a bioinformatics pipeline. In this context, we will plan to assess the performance of various sequence assembly and species delimitation approaches. To determine how well USCOs cover the full length of nuclear genomes and whether or not they perhaps show a tendency to cluster (the latter would have consequences for statistical analyses relying on these genes), we will apply long-read DNA sequencing techniques to determine the position of USCOs in the nuclear genomes of selected species from the investigated groups.

在DFG SPP“分类学” I期资助的项目中，我们建立了一套用于后生动物的核条形码标记物，这些标记基于基因，这些基因几乎完全出现在动物基因组中（通用单复制基因 - USCOS）中。使用靶DNA富集，我们以选定的节肢动物群为例，评估USCOS在划界物种中的适用性和优势。在SPP的第二阶段，我们计划评估USCO条形码方法的鲁棒性，并将其性能与COI条形码的性能进行比较。我们对USCOS的敏锐度特别感兴趣，因为它高估了真实物种的多样性，这一问题已知COI条形码遭受的困扰。为此，我们将增加相对于上一个项目中的基本地理采样，重点是我们在SPP I期中已经对我们已经研究的组：蝴蝶，地窖蜘蛛，cent虫，chafer甲壳虫和悬崖虫。我们还计划研究基因流，这对于经典的条形码方法是不可行的。进行上述研究所需的所有生物信息学步骤都将集成到生物信息学管道中。在这种情况下，我们计划评估各种序列组装和物种划界方法的性能。为了确定USCOS涵盖核基因组的全长程度以及它们是否可能显示出聚类的趋势（后者将对依赖这些基因的统计分析产生后果），我们将采用长阅读的DNA测序技术来确定USCOS在研究组中所选物种的核基因组中的位置。